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Items: 1 to 20 of 200

1.

SEQuel: improving the accuracy of genome assemblies.

Ronen R, Boucher C, Chitsaz H, Pevzner P.

Bioinformatics. 2012 Jun 15;28(12):i188-96. doi: 10.1093/bioinformatics/bts219.

2.

Evaluation of short read metagenomic assembly.

Charuvaka A, Rangwala H.

BMC Genomics. 2011;12 Suppl 2:S8. doi: 10.1186/1471-2164-12-S2-S8. Epub 2011 Jul 27.

3.

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.

Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P.

J Comput Biol. 2011 Nov;18(11):1625-34. doi: 10.1089/cmb.2011.0151. Epub 2011 Oct 14.

4.

Blue: correcting sequencing errors using consensus and context.

Greenfield P, Duesing K, Papanicolaou A, Bauer DC.

Bioinformatics. 2014 Oct;30(19):2723-32. doi: 10.1093/bioinformatics/btu368. Epub 2014 Jun 11.

5.

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D.

Bioinformatics. 2012 Jun 1;28(11):1429-37. doi: 10.1093/bioinformatics/bts175. Epub 2012 Apr 6.

6.

LOCAS--a low coverage assembly tool for resequencing projects.

Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.

PLoS One. 2011;6(8):e23455. doi: 10.1371/journal.pone.0023455. Epub 2011 Aug 15.

7.

QuorUM: An Error Corrector for Illumina Reads.

Marçais G, Yorke JA, Zimin A.

PLoS One. 2015 Jun 17;10(6):e0130821. doi: 10.1371/journal.pone.0130821. eCollection 2015.

8.

Graph accordance of next-generation sequence assemblies.

Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM.

Bioinformatics. 2012 Jan 1;28(1):13-6. doi: 10.1093/bioinformatics/btr588. Epub 2011 Oct 23.

9.

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. doi: 10.1101/gr.7337908. Epub 2008 Mar 13.

10.

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

Li H.

Bioinformatics. 2012 Jul 15;28(14):1838-44. doi: 10.1093/bioinformatics/bts280. Epub 2012 May 7.

11.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

12.

Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C.

Bioinformatics. 2015 Jun 15;31(12):i80-8. doi: 10.1093/bioinformatics/btv262.

13.

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data.

Allam A, Kalnis P, Solovyev V.

Bioinformatics. 2015 Nov 1;31(21):3421-8. doi: 10.1093/bioinformatics/btv415. Epub 2015 Jul 14.

PMID:
26177965
14.

ABRA: improved coding indel detection via assembly-based realignment.

Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.

Bioinformatics. 2014 Oct;30(19):2813-5. doi: 10.1093/bioinformatics/btu376. Epub 2014 Jun 6.

15.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.

16.

A complete bacterial genome assembled de novo using only nanopore sequencing data.

Loman NJ, Quick J, Simpson JT.

Nat Methods. 2015 Aug;12(8):733-5. doi: 10.1038/nmeth.3444. Epub 2015 Jun 15.

PMID:
26076426
17.

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

Shariat B, Movahedi NS, Chitsaz H, Boucher C.

BMC Genomics. 2014;15 Suppl 10:S9. doi: 10.1186/1471-2164-15-S10-S9. Epub 2014 Dec 12.

18.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Kisand V, Lettieri T.

BMC Genomics. 2013 Apr 1;14:211. doi: 10.1186/1471-2164-14-211.

19.

Genome assembly quality: assessment and improvement using the neutral indel model.

Meader S, Hillier LW, Locke D, Ponting CP, Lunter G.

Genome Res. 2010 May;20(5):675-84. doi: 10.1101/gr.096966.109. Epub 2010 Mar 19.

20.

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, Schneider MP, Baumbach J, Tauch A, McCulloch JA, Azevedo VA, Silva A.

J Microbiol Methods. 2011 Aug;86(2):218-23. doi: 10.1016/j.mimet.2011.05.008. Epub 2011 May 18.

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